An evolutionary epigenetic clock in plants.

Area of Science:

• Evolutionary Biology
• Genetics
• Epigenetics

Background:

• Molecular clocks based on DNA sequence divergence are crucial for macro-evolutionary timescales (10^5–10^8 years).
• Classical DNA clocks are too slow to resolve recent evolutionary events and intra-species diversification.
• There is a need for faster molecular clocks to study recent evolutionary history.

Approach:

• Investigated stochastic DNA methylation changes at specific cytosines in plant genomes.
• Characterized the clock-like behavior of these 'epimutation clocks'.
• Validated epimutation clocks using known phylogenetic relationships in *Arabidopsis thaliana* and *Zostera marina*.

Key Points:

• Epimutation clocks operate orders of magnitude faster than DNA-based clocks, enabling dating from years to centuries.
• Demonstrated the utility of epimutation clocks in two distinct plant species with different reproductive strategies: the selfing *A. thaliana* and the clonal seagrass *Z. marina*.
• Epimutation clocks accurately recapitulated established intra-species phylogenetic trees and divergence times.

Conclusions:

• DNA methylation changes provide a novel, rapid molecular clock for evolutionary studies.
• Epimutation clocks offer a powerful new tool for high-resolution temporal studies of plant biodiversity and recent evolution.
• This discovery opens new avenues for understanding plant evolutionary dynamics on contemporary timescales.